[Basel A]

I really doubt your problem is that you bought the wrong gearbox. My first guess would be that you're shifting at the wrong speed. There is an optimal speed for up-shifting and down-shifting. You want to look at the acceleration vs. speed curve for your drivetrain with that gearbox and shift where the curves for the high and low gears cross. This means you won't experience sudden changes in acceleration because they're matched (fun fact: "jerk" is actually the technical term for rate of change of acceleration). This can be done theoretically, but you can also play with it and try different speeds (if you'd like help let me know). Setting these speeds and auto-shifting is highly highly recommended. Also note that (1) the optimal speeds are different for up and down shifting because gearbox efficiency acts differently each way (hurts when accelerating, helps when decelerating) and (2) if you have one shifting speed and you're driving near that speed, it may shift back and forth repeatedly which is not good.

Rahul's question about servo vs. pneumatic shifting gets at another possible reason for that jerk. I don't think pneumatic shifter would have trouble, though.